
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   18 (   72),  selected   18 , name T0386AL243_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   18 , name T0386_D2.pdb
# PARAMETERS: T0386AL243_2-D2.T0386_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       219 - 236         4.99     5.11
  LONGEST_CONTINUOUS_SEGMENT:    17       220 - 237         4.48     5.56
  LCS_AVERAGE:     20.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         1.32     7.82
  LCS_AVERAGE:     13.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       225 - 234         0.60     7.53
  LCS_AVERAGE:      8.98

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   81
LCS_GDT     N     219     N     219      4    7   17     1    4    4    6    7    7    7    7    9    9   13   13   13   16   16   18   18   18   18   18 
LCS_GDT     P     220     P     220      4    7   17     0    4    4    6    7    7    7    8    9   11   14   14   15   17   17   18   18   18   18   18 
LCS_GDT     K     222     K     222      4    7   17     3    4    4    6    7    8    9   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     I     223     I     223      4    7   17     3    4    4    6    7    8    9   11   13   13   14   16   16   17   17   18   18   18   18   18 
LCS_GDT     R     224     R     224      4    7   17     3    4    4    6    7    7    9   11   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     L     225     L     225     10   13   17     7   10   11   11   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     L     226     L     226     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     K     227     K     227     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     E     228     E     228     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     F     229     F     229     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     M     230     M     230     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     H     231     H     231     10   13   17     7   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     T     232     T     232     10   13   17     6   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     M     233     M     233     10   13   17     4   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     K     234     K     234     10   13   17     4   10   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     N     235     N     235      4   13   17     3    4    4   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     T     236     T     236      4   13   17     3    6   11   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     G     237     G     237      3   13   17     3    3    4   12   13   13   13   13   14   14   15   16   16   17   17   18   18   18   18   18 
LCS_AVERAGE  LCS_A:  14.65  (   8.98   13.99   20.99 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      7     10     11     12     13     13     13     13     14     14     15     16     16     17     17     18     18     18     18     18 
GDT PERCENT_CA   8.64  12.35  13.58  14.81  16.05  16.05  16.05  16.05  17.28  17.28  18.52  19.75  19.75  20.99  20.99  22.22  22.22  22.22  22.22  22.22
GDT RMS_LOCAL    0.09   0.60   0.81   1.33   1.32   1.32   1.32   1.32   2.26   2.26   3.17   3.66   3.66   4.48   4.48   5.03   5.03   5.03   5.03   5.03
GDT RMS_ALL_CA   7.35   7.53   7.72   7.96   7.82   7.82   7.82   7.82   7.31   7.31   6.47   5.99   5.99   5.56   5.56   5.03   5.03   5.03   5.03   5.03

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         21.039
LGA    P     220      P     220         17.470
LGA    K     222      K     222         10.884
LGA    I     223      I     223         12.158
LGA    R     224      R     224          7.978
LGA    L     225      L     225          1.127
LGA    L     226      L     226          0.818
LGA    K     227      K     227          0.584
LGA    E     228      E     228          1.027
LGA    F     229      F     229          0.964
LGA    M     230      M     230          0.806
LGA    H     231      H     231          0.991
LGA    T     232      T     232          0.413
LGA    M     233      M     233          0.686
LGA    K     234      K     234          1.457
LGA    N     235      N     235          2.692
LGA    T     236      T     236          1.311
LGA    G     237      G     237          2.237

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   81    4.0     13    1.32    16.358    15.936     0.916

LGA_LOCAL      RMSD =  1.319  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.819  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  5.032  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.481190 * X  +  -0.196345 * Y  +   0.854345 * Z  +  35.151997
  Y_new =  -0.683436 * X  +   0.526304 * Y  +   0.505885 * Z  +  31.449156
  Z_new =  -0.548973 * X  +  -0.827317 * Y  +   0.119062 * Z  + 112.474152 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.427864    1.713729  [ DEG:   -81.8106     98.1894 ]
  Theta =   0.581135    2.560458  [ DEG:    33.2966    146.7034 ]
  Phi   =  -0.957341    2.184252  [ DEG:   -54.8516    125.1484 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0386AL243_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL243_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   81   4.0   13   1.32  15.936     5.03
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL243_2-D2
REMARK Aligment from pdb entry: 2f6sA
ATOM    621  N   ASN   219      12.479  70.595  88.055  1.00  0.00              
ATOM    622  CA  ASN   219      11.313  69.735  87.860  1.00  0.00              
ATOM    623  C   ASN   219      11.645  68.291  88.202  1.00  0.00              
ATOM    624  O   ASN   219      12.777  67.838  87.968  1.00  0.00              
ATOM    625  N   PRO   220      10.654  67.580  88.749  1.00  0.00              
ATOM    626  CA  PRO   220      10.743  66.133  88.991  1.00  0.00              
ATOM    627  C   PRO   220      10.450  65.307  87.737  1.00  0.00              
ATOM    628  O   PRO   220      10.706  64.109  87.699  1.00  0.00              
ATOM    629  N   LYS   222       9.934  65.969  86.713  1.00  0.00              
ATOM    630  CA  LYS   222       9.540  65.316  85.486  1.00  0.00              
ATOM    631  C   LYS   222      10.729  65.081  84.552  1.00  0.00              
ATOM    632  O   LYS   222      10.780  65.598  83.430  1.00  0.00              
ATOM    633  N   ILE   223      11.669  64.269  85.012  1.00  0.00              
ATOM    634  CA  ILE   223      12.993  64.203  84.391  1.00  0.00              
ATOM    635  C   ILE   223      13.029  63.443  83.071  1.00  0.00              
ATOM    636  O   ILE   223      14.070  63.395  82.404  1.00  0.00              
ATOM    637  N   ARG   224      11.902  62.840  82.707  1.00  0.00              
ATOM    638  CA  ARG   224      11.877  61.894  81.604  1.00  0.00              
ATOM    639  C   ARG   224      10.944  62.284  80.468  1.00  0.00              
ATOM    640  O   ARG   224      10.997  61.675  79.401  1.00  0.00              
ATOM    641  N   LEU   225      10.088  63.281  80.696  1.00  0.00              
ATOM    642  CA  LEU   225       9.205  63.769  79.649  1.00  0.00              
ATOM    643  C   LEU   225      10.001  64.335  78.451  1.00  0.00              
ATOM    644  O   LEU   225      10.707  65.356  78.593  1.00  0.00              
ATOM    645  N   LEU   226       9.907  63.682  77.264  1.00  0.00              
ATOM    646  CA  LEU   226      10.798  64.205  76.213  1.00  0.00              
ATOM    647  C   LEU   226      10.334  65.569  75.653  1.00  0.00              
ATOM    648  O   LEU   226      11.178  66.325  75.155  1.00  0.00              
ATOM    649  N   LYS   227       9.041  65.902  75.769  1.00  0.00              
ATOM    650  CA  LYS   227       8.582  67.258  75.403  1.00  0.00              
ATOM    651  C   LYS   227       9.290  68.321  76.267  1.00  0.00              
ATOM    652  O   LYS   227       9.873  69.285  75.745  1.00  0.00              
ATOM    653  N   GLU   228       9.250  68.118  77.585  1.00  0.00              
ATOM    654  CA  GLU   228       9.933  68.973  78.552  1.00  0.00              
ATOM    655  C   GLU   228      11.431  69.091  78.237  1.00  0.00              
ATOM    656  O   GLU   228      12.001  70.177  78.290  1.00  0.00              
ATOM    657  N   PHE   229      12.044  67.964  77.893  1.00  0.00              
ATOM    658  CA  PHE   229      13.465  67.910  77.618  1.00  0.00              
ATOM    659  C   PHE   229      13.817  68.666  76.336  1.00  0.00              
ATOM    660  O   PHE   229      14.801  69.403  76.297  1.00  0.00              
ATOM    661  N   MET   230      12.997  68.504  75.304  1.00  0.00              
ATOM    662  CA  MET   230      13.205  69.199  74.037  1.00  0.00              
ATOM    663  C   MET   230      13.023  70.715  74.197  1.00  0.00              
ATOM    664  O   MET   230      13.846  71.486  73.705  1.00  0.00              
ATOM    665  N   HIS   231      11.967  71.132  74.895  1.00  0.00              
ATOM    666  CA  HIS   231      11.790  72.541  75.245  1.00  0.00              
ATOM    667  C   HIS   231      13.010  73.101  75.970  1.00  0.00              
ATOM    668  O   HIS   231      13.453  74.217  75.685  1.00  0.00              
ATOM    669  N   THR   232      13.556  72.309  76.887  1.00  0.00              
ATOM    670  CA  THR   232      14.753  72.661  77.608  1.00  0.00              
ATOM    671  C   THR   232      15.950  72.866  76.701  1.00  0.00              
ATOM    672  O   THR   232      16.658  73.884  76.806  1.00  0.00              
ATOM    673  N   MET   233      16.188  71.914  75.804  1.00  0.00              
ATOM    674  CA  MET   233      17.365  71.982  74.949  1.00  0.00              
ATOM    675  C   MET   233      17.228  73.082  73.911  1.00  0.00              
ATOM    676  O   MET   233      18.207  73.722  73.572  1.00  0.00              
ATOM    677  N   LYS   234      16.010  73.318  73.424  1.00  0.00              
ATOM    678  CA  LYS   234      15.752  74.415  72.507  1.00  0.00              
ATOM    679  C   LYS   234      16.141  75.739  73.178  1.00  0.00              
ATOM    680  O   LYS   234      16.721  76.611  72.546  1.00  0.00              
ATOM    681  N   ASN   235      15.839  75.885  74.462  1.00  0.00              
ATOM    682  CA  ASN   235      16.159  77.110  75.170  1.00  0.00              
ATOM    683  C   ASN   235      17.667  77.225  75.365  1.00  0.00              
ATOM    684  O   ASN   235      18.240  78.311  75.209  1.00  0.00              
ATOM    685  N   THR   236      18.309  76.097  75.681  1.00  0.00              
ATOM    686  CA  THR   236      19.748  76.060  75.822  1.00  0.00              
ATOM    687  C   THR   236      20.416  76.611  74.553  1.00  0.00              
ATOM    688  O   THR   236      21.337  77.424  74.634  1.00  0.00              
ATOM    689  N   GLY   237      19.944  76.168  73.386  1.00  0.00              
ATOM    690  CA  GLY   237      20.474  76.645  72.102  1.00  0.00              
ATOM    691  C   GLY   237      20.109  78.101  71.838  1.00  0.00              
ATOM    692  O   GLY   237      20.870  78.843  71.204  1.00  0.00              
END
